R script executor

Path	pimlico.modules.r.script
Executable	yes

Simple interface to R that just involves running a given R script, first substituting in some paths from the pipeline, making it easy to pass in data from the output of other modules.

Inputs

Name	Type(s)
sources	list of PimlicoDatatype

Outputs

Name	Type(s)
output	NamedFile()

Options

Name	Description	Type
script	(required) Path to the script to be run. The script itself may include substitutions of the form ‘{{inputX}}’, which will be replaced with the absolute path to the data dir of the Xth input, and ‘{{output}}’, which will be replaced with the absolute path to the output dir. The latter allows the script to output things other than the output file, which always exists and contains the full script’s output	string